Aircraft: MEDIUM TRANSPORT; LOW WING; 2 TURBOJET ENG
Phase of flight: Taxi
Anomaly: ATC Issue All Types; Deviation / Discrepancy - Procedural Published Material / Policy; Ground Event / Encounter Other / Unknown; Ground Incursion Runway

After landing on RWY 8L at HNL we were taxiing to the East Ramp. Tower cleared us to cross RWY 4L and Hold Short of RWY 4R on Delta Taxiway. There are two Hold Short lines on Taxiway Delta between Rwy 4L and 4R which are in close proximity to one another. The two opposing Hold Short lines are different than at most airports with parallel runways adjacent to one another in that the Hold Short line are painted in reverse. At most airports (PDK taxiways between RWY 3L and RWY 3R; MDW taxiways between RWY 4L and RWY 4R; as an example) the aircraft would cross the first runway and proceed across the first painted Hold Short line to stop the aircraft prior to the second painted Hold Short line which is short of the second runway.At HNL on Taxiway Delta between runway 4L and 4R; the intent is for the aircraft stop short of the first painted Hold Short line rather than the second painted Hold Short line. Thus the painted Hold Short lines are reversed or non-standard compared to most airports. It's important to note that stopping short of the first painted Hold Short line in this particular situation leaves the tail of our sized aircraft to overhang the runway (4L in this case) the aircraft was instructed to cross. Having any portion of an aircraft overhanging a runway is not a normal practice given Tower's instructions were to; 'cross runway 4L...' In our confusion with this non-standard set of painted Hold Short lines on Taxiway Delta between Rwy 4L and 4R; we failed to notice the difference and crossed the first painted Hold Short line and held short of RWY 4R at the second painted Hold Short line which required a call to the tower. We contacted the Tower and the Tower stated that this happens a lot at this intersection. Given the Tower's comment it's odd that there are five Hot Spots on this airport; but Taxiway Delta between RWY 4L and RWY 4R is not one of them.Some takeaways to prevent this from occurring again at airport where the painted Hold Short lines are reversed:1) Tower Phraseology - Tower can easily prevent this from occurring again by either waiting to cross the aircraft at a point in time where the aircraft can cross both runways without Holding Short of the second runway or give the following instructions; 'Cross RWY 4L; but Hold Short of the first painted Hold Short lines on Taxiway Delta. Using standard phraseology with non-standard Hold Short markings sets the pilot up for failure unless the pilot is very vigilant.2) Pilots have to be vigilant; identify and confirm the painted Hold Short lines and understand their intent. It's important to note that unless an aircraft departed one of the neighboring Hawaiian Islands; the crew may be on the back side of a long duty day which diminishes a pilot's ability to recognize a non-standard situation similar to this one.As the Tower Controller stated; 'This happens a lot...' and if nothing changes it's probably going to happen again to a good crew that's trying to do the right thing. [Our aircraft] was cleared to cross 4L at Delta and hold short of 4R at PHNL; aircraft nose crossed the first set of hold short lines which with put it in the runway incursion zone. After researching and talking to PHNL tower; I found this is a known hotspot and has the honor of having the top runway incursion of any airport because of this nonstandard situation. At other airports; an aircraft crosses a runway and the first set of hold short lines which are for the runway being crossed and the 2nd second set of lines are for the runway the aircraft is approaching. This is normal or standard; PHNL is the opposite and cause cockpit confusion. Although this is a known problem at PHNL; there are no hotspot markings for taxiway Delta on the taxi chart and tower / ground control doesn't advised the crews to hold short on the first set of lines when given clearance to cross 4L.Solution would be better markings on taxiways; hotspot notation added to taxi charts; and tower ground advises crews of the problem area when giving clearances the runways. After landing at HNL a corporate jet crew was cleared to cross Runway 4L on Taxiway D; hold short of Runway 4R. However; confused they crossed the Runway 4R hold short line when the 4R hold line was approached before the opposite direction 4L hold line.